tbuckley/cabot-search huggingface dataset:
Abstract A012: Investigating the heterogeneity and clinical significance of tumor-associated macrophages in renal cell carcinoma milieu
Authors: Evelyn M. Zavacky, Minjun Kim, Ariel Madrigal, Zohreh Mehrjoo, Jonathon Spicer, Simon Tanguay, Fadi Brimo, Hamed Najafabadi, Yasser Riazalhosseini
Journal: Cancer Research (2023)

Abstract Background: Tumor-associated macrophages (TAMs) exert a range of immunomodulatory functions in the tumor microenvironment (TME) and have been considered key regulators of tumor development. The interactions of TAMs with cancer and stromal cells in the TME have been shown to promote and sustain tumor progression; however, TAMs are largely phenotypically and functionally heterogeneous. Studies at a single-cell level are therefore necessary to understand biological and clinical relevance of heterogeneity of TAMs. Objective: To investigate the heterogeneity of TAM populations in renal cell carcinoma (RCC), the most common form of Kidney cancer, and to determine their connections to patient outcome. Methods and Results: We leverage single-cell RNA sequencing analysis of six primary RCC tumors and three Lung metastatic clear cell RCC (ccRCC) tumors, from which we identified eight TAM and two monocyte clusters shared across all nine patient tissue samples. Differential gene expression and pathway analyses revealed distinct subsets of upregulated genes and cellular pathways activated in each subpopulation. Survival analysis using gene signatures characteristic of each TAM population in datasets of ccRCC tumors (n=533) from TCGA revealed two subpopulations associated with poor patient outcome in ccRCC. Of these, one subpopulation, which we labelled as TAM-8, was characterized by upregulation of pro-inflammatory cytokines, chemokines, and growth factors such as CCL20, CXCL8, and IL1A/B. To our knowledge, this TAM population has not been described in RCC previously. We performed additional in silico functional analyses to further characterize the function of TAM-8 subpopulation, which indicated an active role in promoting immune cell infiltration and angiogenesis via various pro-inflammatory signaling pathways. Conclusion: This study provides new insight into the heterogeneity of TAM populations in RCC and defines CCL20/CXCL8/IL1High TAM-8 population as a potential driver of poor outcome and a candidate therapeutic target. Citation Format: Evelyn M. Zavacky, Minjun Kim, Ariel Madrigal, Zohreh Mehrjoo, Jonathon Spicer, Simon Tanguay, Fadi Brimo, Hamed Najafabadi, Yasser Riazalhosseini. Investigating the heterogeneity and clinical significance of tumor-associated macrophages in renal cell carcinoma milieu [abstract]. In: Proceedings of the AACR Special Conference: Advances in Kidney Cancer Research; 2023 Jun 24-27; Austin, Texas. Philadelphia (PA): AACR; Cancer Res 2023;83(16 Suppl):Abstract nr A012.
Abstract IA027: New advances in the pathogenesis of renal cell carcinoma in tuberous sclerosis and Birt-Hogg-Dubé syndrome
Authors: Elizabeth Henske
Journal: Cancer Research (2023)

Abstract Tuberous Sclerosis Complex (TSC) is caused by either TSC1 or TSC2 mutations, resulting in tumors of the brain, heart, skin, and kidney with hyperactivation of mechanistic target of rapamycin complex 1 (mTORC1). Renal cell carcinomas (RCC) in TSC have chromophobe-like histology features. In TSC2-deficient cells, mTORC1 activity toward its canonical (Raptor-dependent) substrates is increased, while the phosphorylation of non-canonical substrates such as TFEB is decreased, leading to nuclear localization and increased activity of TFEB. Remarkably, treatment with the mTORC1 inhibitor Rapamycin or downregulation of Rheb or Raptor shifts the balance of mTORC1 activity toward the non-canonical substrates in TSC2-deficient cells, leading to increased phosphorylation of TFEB and decreased TFEB activity. Knockout of Tfeb abolishes renal pathology in two mouse models of TSC, indicating that this substrate specificity is the critical mediator of renal disease in TSC. Together, our results indicate that the TSC protein complex controls a critical switch in mTORC1 substrate specificity upstream of Rheb and the Rags, and the effects of rapamycin in TSC are mediated by the paradoxical increased activity of mTORC1 towards the non-canonical target TFEB. These findings may shed light on the sporadic form of chromophobe RCC, which is derived from the renal intercalated cells and has several mysterious features including mitochondrial abundance, whole chromosome losses, and high levels of glutathione (50-100 times higher than matched normal kidney). We hypothesize that hyperactivation of TFEB and/or TFE3 may represent a “missing link” to chromophobe RCC, which highly express lysosomal genes and proteins, thereby connecting chromophobe RCC to TSC-associated and BHD-associated RCC and to translocation RCC. Citation Format: Elizabeth Henske. New advances in the pathogenesis of renal cell carcinoma in tuberous sclerosis and Birt-Hogg-Dubé syndrome [abstract]. In: Proceedings of the AACR Special Conference: Advances in Kidney Cancer Research; 2023 Jun 24-27; Austin, Texas. Philadelphia (PA): AACR; Cancer Res 2023;83(16 Suppl):Abstract nr IA027.
Abstract IA028: Renal medullary carcinoma: Discovery and validation of tailored treatment strategies
Authors: Pavlos Msaouel
Journal: Cancer Research (2023)

Abstract Renal medullary carcinoma (RMC) is a rare but highly aggressive malignancy that predominantly afflicts young individuals of African descent harboring the sickle cell trait and is defined by loss of the SMARCB1 tumor suppressor. Notably, the anti-VEGF and mTOR targeted therapies and standard immune checkpoint inhibitor strategies developed for clear cell renal cell carcinoma (ccRCC) are completely ineffective against RMC. Conversely, platinum-based cytotoxic chemotherapy regimens are the preferred first-line therapy yielding a response rate of 29% and median survival of 13 months from diagnosis. There is clearly a need for tailored treatment strategies for this deadly disease. To meet this challenge, we have developed a dedicated research and clinical team and bench-to-bedside pipeline that supported the comprehensive profiling of patient samples and the development of multiple RMC cell lines, three patient-derived xenografts, and the first genetically engineered mouse model of RMC. These tools informed the development of the first three clinical trials dedicated to RMC (NCT03587662, NCT03274258, and NCT05347212 at clinicaltrials.gov), as well as the establishment of effective second-line, and more recently third-line, therapeutic strategies that produce objective responses and occasionally cures for this deadly disease. Using these approaches, the majority of patients diagnosed with RMC today will survive beyond a year from diagnosis. The progress made has been supported by a passionate patient advocacy group and the awareness raised has resulted in our current clinical volume of caring for 3-5 patients with RMC per week. Emerging insights into the pathophysiology of RMC have allowed us to uncover an "exercise paradox" whereby the hypoxia induced by high-intensity exercise in the setting of sickle cell trait may be the strongest modifiable risk factor for RMC. The unique biological processes behind the exercise paradox also underlie the distinct biological adaptation of RMC to true hypoxia via the loss of SMARCB1, as opposed to the pseudohypoxia observed in ccRCC driven by VHL loss. Whereas pseudohypoxic tumors are sensitive to VEGF targeting, SMARCB1 loss confers resistance to the hypoxia induced by in vivo inhibition of angiogenesis. These insights have allowed us to identify immediately actionable therapeutic targets paving the way for the next generation of clinical trials for RMC. The benchmark goal is to improve the median survival of patients with RMC to 24 months by 2025 and to 5 years by 2030. Citation Format: Pavlos Msaouel. Renal medullary carcinoma: Discovery and validation of tailored treatment strategies [abstract]. In: Proceedings of the AACR Special Conference: Advances in Kidney Cancer Research; 2023 Jun 24-27; Austin, Texas. Philadelphia (PA): AACR; Cancer Res 2023;83(16 Suppl):Abstract nr IA028.
Abstract A015: Injury-associated transcriptional state transitions in early renal carcinogenesis
Authors: Shoko Hirosue, Jianfeng Ge, Leticia Castillon, Paulo Rodrigues, Dóra Bihary, Alyson Speed, Ludovic Wesolowski, Veronica Caraffini, Anne Y. Warren, Grant D. Stewart, Sarah J. Welsh, Thomas J. Mitchell, Athena Matakidou, Fatemeh S. Seyednasrollah, Shamith A. Samarajiwa, Sakari Vanharanta
Journal: Cancer Research (2023)

Abstract This abstract is being presented as a short talk in the scientific program. A full abstract is printed in the Proffered Abstracts section (PR002) of the Conference Program/Proceedings. Citation Format: Shoko Hirosue, Jianfeng Ge, Leticia Castillon, Paulo Rodrigues, Dóra Bihary, Alyson Speed, Ludovic Wesolowski, Veronica Caraffini, Anne Y. Warren, Grant D. Stewart, Sarah J. Welsh, Thomas J. Mitchell, Athena Matakidou, Fatemeh S. Seyednasrollah, Shamith A. Samarajiwa, Sakari Vanharanta. Injury-associated transcriptional state transitions in early renal carcinogenesis [abstract]. In: Proceedings of the AACR Special Conference: Advances in Kidney Cancer Research; 2023 Jun 24-27; Austin, Texas. Philadelphia (PA): AACR; Cancer Res 2023;83(16 Suppl):Abstract nr A015.
Abstract IA016: Remodeling of tumor metabolism by L-2-hydroxyglutarate: Implications for renal cancer growth and progression
Authors: Sunil Sudarshan
Journal: Cancer Research (2023)

Abstract Tumor cells remodel their metabolism to meet their unique demands in order to support tumor growth and progression. However, this reprogramming may create metabolic vulnerabilities. The small molecule L-2-hdroxyglutarate (L-2HG) is commonly elevated in clear cell renal cell carcinoma (ccRCC). Similar to other small molecules elevated in cancer, L-2HG has the potential to regulate gene expression by altering DNA, histone, and/or RNA methylation. Using unbiased profiling methodologies, we find that L-2HG remodels tumoral metabolism in renal cancer cells through the combined effects on histone methylation and RNA N6-methyladenosine (m6A). The combined effects of L-2HG result in a serine liability that renders tumors cells reliant on exogenous serine to support in vitro/vivo tumor growth and redox balance. In agreement with these data, raised L-2HG kidney tumors have reduced expression of serine biosynthetic enzymes. In summary, our data reveal that high L-2HG kidney tumors could be targeted by strategies that limit the availability of this now "essential" amino acid. Citation Format: Sunil Sudarshan. Remodeling of tumor metabolism by L-2-hydroxyglutarate: Implications for renal cancer growth and progression [abstract]. In: Proceedings of the AACR Special Conference: Advances in Kidney Cancer Research; 2023 Jun 24-27; Austin, Texas. Philadelphia (PA): AACR; Cancer Res 2023;83(16 Suppl):Abstract nr IA016.
Abstract IA012: Modelling childhood cancer using organoid technology
Authors: Jarno Drost
Journal: Cancer Research (2023)

Abstract Cancer is still one of the leading causes of disease-related deaths in children. Survivors suffer from side effects of the, in most cases, intensive treatment regimens. Hence, there is an urgent need to develop improved, less toxic therapies. Our vision is that if we understand the processes that underpin the development of childhood cancer, we will facilitate improved cure rates and a better quality of life. However, therapeutic innovation is hampered by the lack of cell models representative of native tumor tissue. The organoid technology has revolutionized cancer research, as it allows for the ‘unlimited’ expansion of healthy and diseased tissue from individual patients in a dish, while retaining essential characteristics of native tissue. Organoids are therefore seen as avatars of the tissues they were derived from (Drost &amp; Clevers, Nat Rev Cancer 2018). We recently succeeded in establishing culture protocols to grow organoids from a wide spectrum of pediatric malignancies such as Wilms tumors, renal cell carcinomas, as well as different rhabdoid tumor and soft tissue sarcoma subtypes. Subjecting our models to a comprehensive molecular profiling, we were able to demonstrate that pediatric cancer organoids retain many features of the tissues they were derived from (Calandrini et al., Nat Commun 2020; Calandrini et al., Cell Rep 2021; Meister et al., EMBO Mol Med 2022; Paassen et al., Oncogene 2023). Thus, we massively expanded the number of relevant pre-clinical in vitro model systems for cancers for which models were rare or even non-existing, including different pediatric kidney cancer subtypes. We use these models in combination with genetic engineering and (single-cell) omics technologies to study the very fundamental processes underlying tumorigenesis with the aim to find new therapies. Citation Format: Jarno Drost. Modelling childhood cancer using organoid technology [abstract]. In: Proceedings of the AACR Special Conference: Advances in Kidney Cancer Research; 2023 Jun 24-27; Austin, Texas. Philadelphia (PA): AACR; Cancer Res 2023;83(16 Suppl):Abstract nr IA012.
Abstract PR009: Linking VHL and SETD2 in a common oncogenic pathway that converges on the mitotic spindle
Authors: Ruhee Dere, Pratim Chowdhury, Sung Yun Jung, Rim Aboulhassane, Manga Motrapu, Xiaoli Wang, Richard Han, Cheryl Walker, Ian Frew, W. Kimryn Rathmell
Journal: Cancer Research (2023)

Abstract Loss of chromosome 3p is a landmark event in clear cell renal cell carcinoma (ccRCC) that results in mono-allelic loss of VHL (von Hippel Lindau) and SETD2 (Set-domain containing 2) (and other tumor suppressors co-located on 3p). Second hits in VHL inactivate this key tumor suppressor initiating tumor progression. SETD2, a histone methyltransferase, was previously shown to have a dual function in methylating both histones and microtubules, thereby contributing to both the histone and tubulin codes. Methylation by SETD2 on microtubules occurs at the mitotic spindle and is essential for normal mitosis and cytokinesis, with loss of SETD2 acting as a strong driver of apoptosis. This raises a conundrum of how cancer cells survive early mono-allelic loss of SETD2, escaping cell death. We have identified the mitotic kinase, Aurora kinase A (AURKA), as a regulator of SETD2. Our data uncover SETD2 as a unique substrate for phosphorylation by AURKA, with mass spectrometry identifying serine 2080 (S2080) as the site of phosphorylation on SETD2. Phospho-SETD2 (S2080) localized at the spindle poles during mitosis, and this specific localization was modulated by AURKA enzymatic activity. Initial observations reveal a role for AURKA driven SETD2 phosphorylation at S2080 in nucleocytoplasmic shuttling of this methyltransferase. Our data suggest that phosphorylation of SETD2 by AURKA contributes to both its methyltransferase (i.e. enzymatic) activity and its geo-spatial location with the cell. Importantly, AURKA expression levels are high in VHL-null cells resulting from an inability of VHL to target AURKA for degradation and our data now highlight a direct link between VHL and SETD2, two tumor suppressors believed to independently drive RCC pathogenesis. In summary, our data reveal a tumor-specific vulnerability linked to mitotic fragility that can be precisely targeted to ultimately drive mitotic catastrophe. Citation Format: Ruhee Dere, Pratim Chowdhury, Sung Yun Jung, Rim Aboulhassane, Manga Motrapu, Xiaoli Wang, Richard Han, Cheryl Walker, Ian Frew, W. Kimryn Rathmell. Linking VHL and SETD2 in a common oncogenic pathway that converges on the mitotic spindle [abstract]. In: Proceedings of the AACR Special Conference: Advances in Kidney Cancer Research; 2023 Jun 24-27; Austin, Texas. Philadelphia (PA): AACR; Cancer Res 2023;83(16 Suppl):Abstract nr PR009.
Abstract IA017: Metabolic reprogramming and kidney cancer progression
Authors: Ralph J. DeBerardinis
Journal: Cancer Research (2023)

Abstract Many human diseases, including cancer, involve alterations of cellular metabolism caused either directly or indirectly by mutations in genes that regulate the metabolic network. In cancer, reprogrammed metabolic activities arising from mutations in tumor suppressors and oncogenes are thought to contribute both to cancer initiation and progression, particularly metastasis. In clear cell renal cell carcinoma, as with many other kinds of cancer, mortality is largely dictated by metastatic dissemination. It is therefore of interest to identify aspects of metabolic reprogramming that promote metastasis in ccRCC patients. We used a multidisciplinary clinical approach to infuse 13C-labeled nutrients during surgical tumor resection in ccRCC patients. Compared to the adjacent kidney, ccRCCs displayed suppressed labelling of tricarboxylic acid (TCA) cycle intermediates, both in vivo and in organotypic slices cultured ex vivo, indicating that suppressed labeling is a tissue intrinsic property of these tumors. Infusions of 13C-acetate and 13C-glutamine in patients, coupled with metabolic analysis of mitochondria isolated from kidney and tumor tissue, revealed primary defects in mitochondrial function in human ccRCC. However, ccRCC metastases unexpectedly had enhanced labeling of TCA cycle intermediates compared to primary ccRCCs, indicating a divergent metabolic program during ccRCC metastasis in patients. Using a syngeneic RCC mouse model capable of spontaneous metastasis from the kidney, we found that inhibiting oxidative phosphorylation reduced metastasis to the lung without impacting tumor growth in the kidney. In human ccRCC cells, stimulating respiration was sufficient to promote metastatic colonization in the lung. Altogether, these findings indicate that metabolic properties evolve during human ccRCC progression, and suggest that mitochondrial respiration may be limiting for ccRCC metastasis but not for ccRCC growth at the site of origin. Citation Format: Ralph J. DeBerardinis. Metabolic reprogramming and kidney cancer progression [abstract]. In: Proceedings of the AACR Special Conference: Advances in Kidney Cancer Research; 2023 Jun 24-27; Austin, Texas. Philadelphia (PA): AACR; Cancer Res 2023;83(16 Suppl):Abstract nr IA017.
Abstract A014: Modeling recurrent chromosomal alterations in renal cell carcinoma evolution
Authors: Rashmi Dahiya, Peter Ly
Journal: Cancer Research (2023)

Abstract The loss of one copy of chromosome 3p represents an early truncal genetic event in the majority of clear cell renal cell carcinoma (ccRCC) tumors. Chromosome 3p loss can be initiated by chromothripsis, a process in which mis-segregated chromosomes entrapped within abnormal nuclear structures called micronuclei become pulverized into small genomic fragments. These fragments are then re-stitched together to form complex rearrangements that are accompanied by extensive segmental deletions that inactivate critical tumor suppressor genes located on chromosome 3p. Despite being a driver of ccRCC development, the mechanism(s) that initiate chromosome 3p chromothripsis followed by pressures that select for specific rearrangement patterns are poorly understood. To recapitulate early genetic events arising throughout ccRCC evolution, here we developed chromosome 3p-specific micronuclei models in non-transformed human renal proximal tubule epithelial cells (RPTECs) to interrogate recurrent patterns of chromosomal alterations that promote renal cell tumorigenesis. To do so, we used CRISPR/Cas9 to induce a DNA double-strand break on chromosome 3p, which generates chromosome 3p-specific micronuclei when the acentric arm is left unrepaired into the subsequent mitosis. DNA fluorescence in situ hybridization revealed that mis-segregation of chromosome 3p into micronuclei induces chromosome pulverization and rearrangements. Notably, these alterations are sufficient to provide a selective advantage by enabling anchorage-independent growth in vitro. Cytogenetic characterization of partially transformed RPTECs revealed enrichment of chromosome 3p rearrangements, which were gradually lost upon propagation as conventional monolayer cultures. These results provide mechanistic insight into the origins of chromosome 3p alterations in ccRCC and further highlight the role of selection pressure in shaping genome evolution. Citation Format: Rashmi Dahiya, Peter Ly. Modeling recurrent chromosomal alterations in renal cell carcinoma evolution [abstract]. In: Proceedings of the AACR Special Conference: Advances in Kidney Cancer Research; 2023 Jun 24-27; Austin, Texas. Philadelphia (PA): AACR; Cancer Res 2023;83(16 Suppl):Abstract nr A014.
Abstract A009: Therapeutic targeting of P2 × 4 receptor and mitochondrial metabolism in clear cell renal carcinoma
Authors: Sabrina Orsi, Christopher Rupert, Roberto Pili, Filomena De Nigris
Journal: Cancer Research (2023)

Abstract Clear cell renal cell carcinoma (ccRCC) is the most common subtype of kidney cancer. Large scale metabolomic data have associated metabolic alterations with the pathogenesis and progression of renal carcinoma and have correlated mitochondrial activity with poor survival in a subset of patients. Our data suggest that oxo-phosphorylation is the main source of tumor-derived ATP in ccRCC expressing P2XR4, which exerts a critical impact on tumor energy metabolism and mitochondrial activity. Seahorse experiments showed that P2XR4 inhibition by 5-BDBD, a potent selective antagonist, caused a rapid dose-dependent reduction of mitochondrial activity and lysosome damage. Moreover, prolonged mitochondrial failure induced by 5-BDBD or P2XR4 silencing was associated with increased oxygen radical species, changes in mitochondrial permeability (i.e. opening of the transition pore complex, dissipation of membrane potential and calcium overload), and cell death via both necrosis and apoptosis. P2XR4 pharmacological inhibition was associated with a significant anti-tumor effect both in vitro and in vivo, as shown in ccRCC cell lines, patient-derived organoids and in murine xenografts. Interestingly, higher mitochondrial activity was associated with greater sensitivity to P2XR4 inhibition. Overall, our results suggest that the perturbed balance between lysosomal integrity and mitochondrial activity induced by P2XR4 inhibition may represent a new therapeutic strategy for a subset of renal carcinoma patients. Citation Format: Sabrina Orsi, Christopher Rupert, Roberto Pili, Filomena De Nigris. Therapeutic targeting of P2 × 4 receptor and mitochondrial metabolism in clear cell renal carcinoma [abstract]. In: Proceedings of the AACR Special Conference: Advances in Kidney Cancer Research; 2023 Jun 24-27; Austin, Texas. Philadelphia (PA): AACR; Cancer Res 2023;83(16 Suppl):Abstract nr A009.